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Katie Sandlin

Genomic Neighborhood Check For Understanding

This was created in response to a member mentioning their students really struggled with the genomic neighborhood and the member didn’t realize until they were already too far into the annotation to correct their misconceptions. This is meant to be a quick in-class and/or homework assignment.

Pathways Project: Annotation Form

This “Annotation Form” merged the “Annotation Report” and “Annotation Notebook” into a single document and the latter two items were archived.

The “Annotation Form” kept many of the Checks for Understanding type questions that were previously in the “Annotation Notebook.” However, given that not all faculty want their students to answer those questions, we marked any question that is NOT required for submission to the GEP as “OPTIONAL.” Currently the optional questions are organized as letters rather than numbers, which we hope will make it easy to quickly select and delete the OPTIONAL questions that faculty don’t wish to include. Again, all numbered questions are required for submission to the GEP for reconciliation.

Items that were previously asked for in the “Project Details” table of the “Annotation Report” are now available on the Genome Browser Gateway page for each species. Therefore, the “Project Details Table” instructions document is no longer needed.

Pathways Project: Annotation Workflow

The Annotation Workflow is a one page summary of the annotation protocol for the Pathways Project. This workflow provides an overview of the key analysis steps and bioinformatics tools for the annotation of a putative ortholog.

Pathways Project: Annotation Notebook

The Pathways Annotation Notebook will help GEP students keep track of their work as they are annotating, and then they can use the notebook to fill out the report form. This notebook does not have to be submitted to GEP, it’s just an extra resource students might find helpful.